Providencia alcalifaciens (DSM 30120, ATCC 9886, CCUG 6325)

Name: Providencia alcalifaciens (DSM 30120, ATCC 9886, CCUG 6325)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5074

Type strain

Culture col. no. DSM 30120 ATCC 9886 CCUG 6325 NCTC 10286 NBRC 105687 4 more

NCBI tax ID(s) 520999 126385

Special Collections DSMZ CCUG JCM CIP

Links

Providencia alcalifaciens DSM 30120 is an aerobe, mesophilic human pathogen that was isolated from faeces.

aerobe mesophilic human pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 10835

LMG 7878,ATCC 9886,CCUG 6325,DSM 30120,NCTC 10286,JCM 1673,CCRC 13995,CECT 166,BCRC 13995,CIP 82.90

@ref 20215

Last LPSN update 2025-12-16 09:47:59

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Morganellaceae

Genus Providencia

Species Providencia alcalifaciens

Full scientific name Providencia alcalifaciens (de Salles Gomes 1944) Ewing 1962 (Approved Lists 1980)

Synonyms (3)

"Bacillus inconstans"
"Eberthella alcalifaciens"
Proteus inconstans

BacDive ID	Other strains from **Providencia alcalifaciens** (8)	Type strain
136244	P. alcalifaciens B 81, CIP 53.47, NCTC 6345
137659	P. alcalifaciens B 105, CIP 53.43, NCTC 6344
139477	P. alcalifaciens PP 110, CIP 58.62
141235	P. alcalifaciens CCUG 337 B
143594	P. alcalifaciens CCUG 20517 B
147427	P. alcalifaciens CCUG 33571
151035	P. alcalifaciens CCUG 43121
151759	P. alcalifaciens CCUG 44809

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	100

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9143	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
9143	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
37725	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
116205	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
9143	positive	growth	37	mesophilic
37725	positive	growth	30	mesophilic
44887	positive	growth	30-37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

44887

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.76

Compound production

9143

Compoundrestriction endonuclease PalI

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	+	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		+	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	+	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
9143	-	-	-	-	+	-	-	+	+	+	-	+	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type
9143	faeces
44887	Human feces
67770	Feces
116205	Faeces

Taxonmaps

69479

Global distribution of 16S sequence DQ885261 (>99% sequence identity) for Providencia from Microbeatlas

Aquatic Samples	44
Soil Samples	23
Animal Samples	258
Plant Samples	48
Total Samples	373

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
9143			2	Risk group (German classification) According to TRBA 466
116205			2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM17341v1 assembly for Providencia alcalifaciens DSM 30120	contig	GCA_000173415	520999.6	642979317	520999	62.79
66792	31289_D01 assembly for Providencia alcalifaciens NCTC10286	complete	GCA_900478095	126385.9	8116455957	126385	61.45

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Providencia alcalifaciens 16S rRNA gene, strain CIP8290T	AJ301684	1507	520999
20218	Providencia alcalifaciens strain DSM 30120 16S ribosomal RNA gene, partial sequence	EU587047	978	520999
20218	Providencia alcalifaciens DSM 30120 strain NCTC 10286 16S ribosomal RNA gene, partial sequence	DQ885261	1479	520999
124043	Providencia alcalifaciens gene for 16S rRNA, partial sequence, strain: NBRC 105687.	AB682262	1466	126385

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Providencia alcalifaciens strain NCTC10286
PATRIC: 126385.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	70.10	no
125439	gram_stain	BacteriaNetⓘ	negative	67.80	no
125439	motility	BacteriaNetⓘ	no	51.20	no
125439	spore_formation	BacteriaNetⓘ	no	89.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Providencia alcalifaciens NCTC10286
NCBI: GCA_900478095.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	94.97	no
125438	aerobic	aerobicⓘ	no	61.72	yes
125438	spore-forming	spore-formingⓘ	no	90.76	no
125438	thermophilic	thermophileⓘ	no	98.75	yes
125438	flagellated	motile2+ⓘ	yes	71.09	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic revisitation and reclassification of the genus Providencia.	Dong X, Jia H, Yu Y, Xiang Y, Zhang Y.	mSphere	10.1128/msphere.00731-23	2024
	The gene expression and bioinformatic analysis of choline trimethylamine-lyase (CutC) and its activating enzyme (CutD) for gut microbes and comparison with their TMA production levels.	Ramireddy L, Tsen HY, Chiang YC, Hung CY, Chen FC, Yen HT.	Curr Res Microb Sci	10.1016/j.crmicr.2021.100043	2021
Genetics	Genome sequencing and annotation of Morganella sp. SA36.	Selim S, Hassan S, Hagagy N.	Genom Data	10.1016/j.gdata.2015.08.016	2015
	Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator.	Saeedi A, Cummings NJ, McLean D, Connerton IF, Connerton PL.	Sci Rep	10.1038/s41598-021-00865-8	2021
	Comparative genomics of bacteria in the genus Providencia isolated from wild Drosophila melanogaster.	Galac MR, Lazzaro BP.	BMC Genomics	10.1186/1471-2164-13-612	2012
Metabolism	Functional identification of Proteus mirabilis eptC gene encoding a core lipopolysaccharide phosphoethanolamine transferase.	Aquilini E, Merino S, Knirel YA, Regue M, Tomas JM.	Int J Mol Sci	10.3390/ijms15046689	2014
Pathogenicity	Synergy and remarkable specificity of antimicrobial peptides in vivo using a systematic knockout approach.	Hanson MA, Dostalova A, Ceroni C, Poidevin M, Kondo S, Lemaitre B.	Elife	10.7554/elife.44341	2019
Pathogenicity	AIP56: a novel bacterial apoptogenic toxin.	Silva MT, Dos Santos NM, do Vale A.	Toxins (Basel)	10.3390/toxins2040905	2010
	BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.	Rasko T, Der A, Klement E, Slaska-Kiss K, Posfai E, Medzihradszky KF, Marshak DR, Roberts RJ, Kiss A.	Nucleic Acids Res	10.1093/nar/gkq567	2010
	The O28 Antigen Gene Clusters of Salmonella enterica subsp. enterica Serovar Dakar and Serovar Pomona Are Different.	Clark CG, Grant CC, Trout-Yakel KM, Tabor H, Ng LK, Rahn K, Franklin K, Kropinski AM.	Int J Microbiol	10.1155/2010/209291	2010
Phylogeny	Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.	Shlykov MA, Zheng WH, Chen JS, Saier MH.	Biochim Biophys Acta	10.1016/j.bbamem.2011.12.005	2012
	Inactivation of Burkholderia cepacia complex phage KS9 gp41 identifies the phage repressor and generates lytic virions.	Lynch KH, Seed KD, Stothard P, Dennis JJ, Dennis JJ.	J Virol	10.1128/jvi.01843-09	2010
Enzymology	The abundance of Zoogloea ramigera in sewage treatment plants.	Rossello-Mora RA, Wagner M, Amann R, Schleifer KH.	Appl Environ Microbiol	10.1128/aem.61.2.702-707.1995	1995
	In Vitro and In Vivo Properties of CUO246, a Novel Bacterial DNA Gyrase/Topoisomerase IV Inhibitor.	Blais J, Dean CR, Lapointe G, Leeds JA, Ma S, Morris L, Moser HE, Osborne CS, Prosen KR, Richie D, Skepper C, Thompson K, Vo J, Yue Q, Rivkin A.	Antimicrob Agents Chemother	10.1128/aac.00921-22	2022
	Sansanmycin natural product analogues as potent and selective anti-mycobacterials that inhibit lipid I biosynthesis.	Tran AT, Watson EE, Pujari V, Conroy T, Dowman LJ, Giltrap AM, Pang A, Wong WR, Linington RG, Mahapatra S, Saunders J, Charman SA, West NP, Bugg TD, Tod J, Dowson CG, Roper DI, Crick DC, Britton WJ, Payne RJ.	Nat Commun	10.1038/ncomms14414	2017
Biotechnology	Rapid separation and concentration of food-borne pathogens in food samples prior to quantification by viable-cell counting and real-time PCR.	Fukushima H, Katsube K, Hata Y, Kishi R, Fujiwara S.	Appl Environ Microbiol	10.1128/aem.01772-06	2007
	Description of a 2,683-base-pair plasmid containing qnrD in two Providencia rettgeri isolates.	Guillard T, Cambau E, Neuwirth C, Nenninger T, Mbadi A, Brasme L, Vernet-Garnier V, Bajolet O, de Champs C.	Antimicrob Agents Chemother	10.1128/aac.00081-11	2012
Pathogenicity	In Vitro Antibacterial Properties of Cefiderocol, a Novel Siderophore Cephalosporin, against Gram-Negative Bacteria.	Ito A, Sato T, Ota M, Takemura M, Nishikawa T, Toba S, Kohira N, Miyagawa S, Ishibashi N, Matsumoto S, Nakamura R, Tsuji M, Yamano Y.	Antimicrob Agents Chemother	10.1128/aac.01454-17	2018
Enzymology	Sloth hair as a novel source of fungi with potent anti-parasitic, anti-cancer and anti-bacterial bioactivity.	Higginbotham S, Wong WR, Linington RG, Spadafora C, Iturrado L, Arnold AE.	PLoS One	10.1371/journal.pone.0084549	2014
	Mobile insertion cassette elements found in small non-transmissible plasmids in Proteeae may explain qnrD mobilization.	Guillard T, Grillon A, de Champs C, Cartier C, Madoux J, Bercot B, Lebreil AL, Lozniewski A, Riahi J, Vernet-Garnier V, Cambau E.	PLoS One	10.1371/journal.pone.0087801	2014
Enzymology	Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species.	Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG.	J Clin Microbiol	10.1128/jcm.42.8.3686-3695.2004	2004
Enzymology	Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples.	Maheux AF, Bissonnette L, Boissinot M, Bernier JL, Huppe V, Picard FJ, Berube E, Bergeron MG.	Appl Environ Microbiol	10.1128/aem.02337-10	2011
	Development of a PCR assay for rapid detection of enterococci.	Ke D, Picard FJ, Martineau F, Menard C, Roy PH, Ouellette M, Bergeron MG.	J Clin Microbiol	10.1128/jcm.37.11.3497-3503.1999	1999
Pathogenicity	In vitro model of colonization resistance by the enteric microbiota: effects of antimicrobial agents used in food-producing animals.	Wagner RD, Johnson SJ, Cerniglia CE.	Antimicrob Agents Chemother	10.1128/aac.00852-07	2008
Enzymology	Description and evaluation of the semiautomated 4-hour ATB 32E method for identification of members of the family Enterobacteriaceae.	Freney J, Herve C, Desmonceaux M, Allard F, Boeufgras JM, Monget D, Fleurette J.	J Clin Microbiol	10.1128/jcm.29.1.138-141.1991	1991
Metabolism	Extent of peptidoglycan O acetylation in the tribe Proteeae.	Clarke AJ.	J Bacteriol	10.1128/jb.175.14.4550-4553.1993	1993
Phylogeny	Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria.	Ahmad S, Weisburg WG, Jensen RA.	J Bacteriol	10.1128/jb.172.2.1051-1061.1990	1990
	Bacteriocins as tools in analysis of nosocomial Klebsiella pneumoniae infections.	Bauernfeind A, Petermuller C, Schneider R.	J Clin Microbiol	10.1128/jcm.14.1.15-19.1981	1981
Metabolism	Pharmacokinetic evaluation of ceftiofur in serum, tissue chamber fluid and bronchial secretions from healthy beef-bred calves.	Halstead SL, Walker RD, Baker JC, Holland RE, Stein GE, Hauptman JG.	Can J Vet Res		1992
Phylogeny	Molecular characterization of the genera Proteus, Morganella, and Providencia by ribotyping.	Pignato S, Giammanco GM, Grimont F, Grimont PA, Giammanco G.	J Clin Microbiol	10.1128/jcm.37.9.2840-2847.1999	1999
Genetics	Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes.	Chen YT, Peng HL, Shia WC, Hsu FR, Ken CF, Tsao YM, Chen CH, Liu CE, Hsieh MF, Chen HC, Tang CY, Ku TH.	BMC Genomics	10.1186/1471-2164-13-s7-s4	2012
Phylogeny	Kit systems for identifying gram negative aerobic bacilli: report of the Welsh Standing Specialist Advisory Working Group in Microbiology.	Bennett CH, Joynson DH.	J Clin Pathol	10.1136/jcp.39.6.666	1986
	Molecular Identification and Selection of Probiotic Strains Able to Reduce the Serum TMAO Level in Mice Challenged with Choline.	Ramireddy L, Tsen HY, Chiang YC, Hung CY, Wu SR, Young SL, Lin JS, Huang CH, Chiu SH, Chen CC, Chen CC.	Foods	10.3390/foods10122931	2021
	Taxonomic and phenotypic characterization of a novel Providencia species: Providencia lanzhouensis sp. nov.	Xiang Y, Dong X, Ma L, Cao D, Li Y, Jiang X, Xu P, Yuan X, Bi K, Zhang Y, Han Y, Zhang Y.	Microbiol Spectr	10.1128/spectrum.00549-25	2025
	Novel Providencia xianensis sp. nov.: A multidrug-resistant species identified in clinical infections.	Dong X, Xiang Y, Yang P, Wang S, Yan W, Yuan Y, Zhou S, Zhou K, Liu J, Zhang Y.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-024-04821-y	2024

References

#9143	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30120
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#37725	; Curators of the CIP;
#44887	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 6325
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#116205	Collection of Institut Pasteur ; Curators of the CIP; CIP 82.90
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Providencia alcalifaciens (DSM 30120, ATCC 9886, CCUG 6325)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000173415

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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